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(-) Description

Title :  PBP ACCA FROM A. TUMEFACIENS C58
 
Authors :  A. El Sahili, S. Morera
Date :  20 Apr 15  (Deposition) - 19 Aug 15  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Pbp From C Cluster, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. El Sahili, S. Z. Li, J. Lang, C. Virus, S. Planamente, M. Ahmar, B. G. Guimaraes, M. Aumont-Nicaise, A. Vigouroux, L. Soulere, J. Reader, Y. Queneau, D. Faure, S. Morera
A Pyranose-2-Phosphate Motif Is Responsible For Both Antibiotic Import And Quorum-Sensing Regulation In Agrobacterium Tumefaciens.
Plos Pathog. V. 11 05071 2015
PubMed-ID: 26244338  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1005071

(-) Compounds

Molecule 1 - ABC TRANSPORTER, SUBSTRATE BINDING PROTEIN (AGROCINOPINES A AND B)
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 30-521
    Gene: ACCA, ATU6139
    Organism Scientific: AGROBACTERIUM TUMEFACIENS (STRAIN C58 / ATCC 33970)
    Organism Taxid: 176299

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4SO46Ligand/IonSULFATE ION
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4SO41Ligand/IonSULFATE ION
Biological Unit 4 (3, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4SO41Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:31 , ARG A:32 , SER A:233 , HOH A:863 , ARG C:163binding site for residue SO4 A 601
02AC2SOFTWAREARG A:163 , HOH A:937 , GLU C:31 , ARG C:32 , SER C:233 , HOH C:1077 , HOH C:1187binding site for residue SO4 A 602
03AC3SOFTWAREPRO A:450 , ALA A:451 , HOH A:703 , HOH A:1026binding site for residue SO4 A 603
04AC4SOFTWAREASN A:311 , TYR A:348 , GLN A:392 , HOH A:754 , HOH A:776 , HOH A:984binding site for residue EDO A 604
05AC5SOFTWAREALA A:69 , ARG A:70 , ASP A:71 , ARG A:515 , HOH A:827 , HOH A:846binding site for residue PEG A 605
06AC6SOFTWARETYR A:402 , PHE A:407 , ARG A:416 , ASN A:417 , TRP A:418 , GLN A:440 , TRP A:445 , HOH A:701 , HOH A:877binding site for residue GOL A 606
07AC7SOFTWARESER A:177 , TRP A:178 , TRP A:423 , PHE A:509 , HOH A:798binding site for residue EDO A 607
08AC8SOFTWAREARG B:163 , HOH B:851binding site for residue SO4 B 601
09AC9SOFTWARETYR B:145 , ASN B:420 , GLY B:421 , THR B:430 , GLU B:434 , HOH B:866binding site for residue EDO B 602
10AD1SOFTWAREGLY B:227 , PRO B:228 , LYS B:229 , HOH B:713 , LYS C:344 , HOH C:1140binding site for residue EDO B 603
11AD2SOFTWAREALA B:69 , ARG B:70 , ARG B:515 , HOH B:702 , HOH B:794 , HOH B:958 , HOH B:1011binding site for residue EDO B 604
12AD3SOFTWARELYS B:500 , GLY C:466 , LYS C:467 , GLU C:468 , HOH C:739 , HOH C:978 , HOH C:1041binding site for residue SO4 C 601
13AD4SOFTWARESER C:177 , TRP C:178 , TRP C:423 , PHE C:509 , HOH C:715 , HOH C:801binding site for residue EDO C 602
14AD5SOFTWAREASP B:340 , ASN B:474 , HOH B:810 , SER C:519 , HOH C:862binding site for residue EDO C 603
15AD6SOFTWAREARG D:163binding site for residue SO4 D 601
16AD7SOFTWAREALA D:69 , ARG D:70 , ASP D:71 , ARG D:515 , HOH D:752 , HOH D:768 , HOH D:773 , HOH D:799binding site for residue GOL D 602
17AD8SOFTWAREHIS D:111 , ASP D:112 , PHE D:208binding site for residue EDO D 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZE8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:429 -Thr A:430
2Ala B:429 -Thr B:430
3Ala C:429 -Thr C:430
4Ala D:429 -Thr D:430

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZE8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZE8)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZE8)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:491
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee................hhhhhhhhh...eee..hhhhh......eee..eeeeeeee..eeeeee............hhhhhhhhh........hhhhhh.........eeeeeeee..eeeeee.....hhhhhh........hhhhhhhhhhhhhhhh......eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeeeehhhhhhhhh....eeeeeee..eeeeeee...hhhhhhhhhhhhhhhh.hhhhhhhhhhh..........hhhhhhhh.........hhhhhhhhhhhh......eeeee......hhhhhhhhhhhhhhh....eeeee.......hhhhh.eeeeeee.....hhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeeee..eeeeeee...................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ze8 A  31 ERRALRLGVNGLPNSLEPVNAISNVGPRIVNQIFDTLIARDFFAKGAPGNAIDLVPALAESWERIDEKSVRFKLRQKVMFHDGVELTADDVAYTFSSERLWGPEAIKKIPLGKSYSLDFDEPVVEDKYTVTLRTKTPSYLIETFVASWMSRIVPKEYYKKLGAVDFGNKPVGTGPYKFVEFVAGDRVVLEANDAYWGPKPTASKITYQIVAEPATRVAGLISGEYDIITTLTPDDIQLINSYPDLETRGTLIENFHMFTFNMNQEVFKDKKLRRALALAVNRPIMVEALWKKQASIPAGFNFPNYGETFDPKRKAMEYNVEEAKRLVKESGYDGTPITYHTMGNYYANAMPALMMMIEMWKQIGVNVVMKTYAPGSFPPDNQTWMRNWSNGQWMTDAYATIVPEFGPNGQVQKRWGWKAPAEFNELCQKVTVLPNGKERFDAYNRMRDIFEEEAPAVILYQPYDVYAARKDVHWKPVSFEMMEFRNNLSFG 521
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520 


Chain B from PDB  Type:PROTEIN  Length:491
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee................hhhhhhhhh...eee..hhhhh......eee..eeeeeeee..eeeeee............hhhhhhhhh......hhhhh............eeeeeeee..eeeeee.....hhhhhh........hhhhhhhhhhhhhhhh......eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeeeehhhhhhhhhh...eeeeeee..eeeeeee...hhhhhhhhhhhhhhhh.hhhhhhhhhhh..........hhhhhhhh.........hhhhhhhhhhhh......eeeee......hhhhhhhhhhhhhhh....eeeee.......hhhhh.eeeeeee.....hhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeeee..eeeeeee..ee...............ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ze8 B  31 ERRALRLGVNGLPNSLEPVNAISNVGPRIVNQIFDTLIARDFFAKGAPGNAIDLVPALAESWERIDEKSVRFKLRQKVMFHDGVELTADDVAYTFSSERLWGPEAIKKIPLGKSYSLDFDEPVVEDKYTVTLRTKTPSYLIETFVASWMSRIVPKEYYKKLGAVDFGNKPVGTGPYKFVEFVAGDRVVLEANDAYWGPKPTASKITYQIVAEPATRVAGLISGEYDIITTLTPDDIQLINSYPDLETRGTLIENFHMFTFNMNQEVFKDKKLRRALALAVNRPIMVEALWKKQASIPAGFNFPNYGETFDPKRKAMEYNVEEAKRLVKESGYDGTPITYHTMGNYYANAMPALMMMIEMWKQIGVNVVMKTYAPGSFPPDNQTWMRNWSNGQWMTDAYATIVPEFGPNGQVQKRWGWKAPAEFNELCQKVTVLPNGKERFDAYNRMRDIFEEEAPAVILYQPYDVYAARKDVHWKPVSFEMMEFRNNLSFG 521
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520 


Chain C from PDB  Type:PROTEIN  Length:491
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee................hhhhhhhhh...eee..hhhhh......eee..eeeeeeee..eeeeee............hhhhhhhhh......hhhhh............eeeeeeee..eeeeee.....hhhhhh........hhhhhhhhhhhhhhhh......eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeeeehhhhhhhhh....eeeeeee..eeeeeee...hhhhhhhhhhhhhhhh.hhhhhhhhhhh..........hhhhhhhh.........hhhhhhhhhhhh......eeeee......hhhhhhhhhhhhhhhh...eeeee.......hhhhh.eeeeeee.....hhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeeee..eeeeeee..ee...............ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ze8 C  31 ERRALRLGVNGLPNSLEPVNAISNVGPRIVNQIFDTLIARDFFAKGAPGNAIDLVPALAESWERIDEKSVRFKLRQKVMFHDGVELTADDVAYTFSSERLWGPEAIKKIPLGKSYSLDFDEPVVEDKYTVTLRTKTPSYLIETFVASWMSRIVPKEYYKKLGAVDFGNKPVGTGPYKFVEFVAGDRVVLEANDAYWGPKPTASKITYQIVAEPATRVAGLISGEYDIITTLTPDDIQLINSYPDLETRGTLIENFHMFTFNMNQEVFKDKKLRRALALAVNRPIMVEALWKKQASIPAGFNFPNYGETFDPKRKAMEYNVEEAKRLVKESGYDGTPITYHTMGNYYANAMPALMMMIEMWKQIGVNVVMKTYAPGSFPPDNQTWMRNWSNGQWMTDAYATIVPEFGPNGQVQKRWGWKAPAEFNELCQKVTVLPNGKERFDAYNRMRDIFEEEAPAVILYQPYDVYAARKDVHWKPVSFEMMEFRNNLSFG 521
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520 


Chain D from PDB  Type:PROTEIN  Length:491
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee................hhhhhhhhh...eee..hhhhh......eee..eeeeeeee..eeeeee............hhhhhhhhh........hhhhhh.........eeeeeeee..eeeeee.....hhhhhh........hhhhhhhhhhhhhhhh......eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeeeehhhhhhhhhh...eeeeeee..eeeeeee...hhhhhhhhhhhhhhhh.hhhhhhhhhhh..........hhhhhhhh.........hhhhhhhhhhhh......eeeee......hhhhhhhhhhhhhhh....eeeee.......hhhhh.eeeeeee.....hhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeeee..eeeeeee..ee...............ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ze8 D  31 ERRALRLGVNGLPNSLEPVNAISNVGPRIVNQIFDTLIARDFFAKGAPGNAIDLVPALAESWERIDEKSVRFKLRQKVMFHDGVELTADDVAYTFSSERLWGPEAIKKIPLGKSYSLDFDEPVVEDKYTVTLRTKTPSYLIETFVASWMSRIVPKEYYKKLGAVDFGNKPVGTGPYKFVEFVAGDRVVLEANDAYWGPKPTASKITYQIVAEPATRVAGLISGEYDIITTLTPDDIQLINSYPDLETRGTLIENFHMFTFNMNQEVFKDKKLRRALALAVNRPIMVEALWKKQASIPAGFNFPNYGETFDPKRKAMEYNVEEAKRLVKESGYDGTPITYHTMGNYYANAMPALMMMIEMWKQIGVNVVMKTYAPGSFPPDNQTWMRNWSNGQWMTDAYATIVPEFGPNGQVQKRWGWKAPAEFNELCQKVTVLPNGKERFDAYNRMRDIFEEEAPAVILYQPYDVYAARKDVHWKPVSFEMMEFRNNLSFG 521
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4ZE8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZE8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZE8)

(-) Gene Ontology  (2, 2)

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  Cis Peptide Bonds
    Ala A:429 - Thr A:430   [ RasMol ]  
    Ala B:429 - Thr B:430   [ RasMol ]  
    Ala C:429 - Thr C:430   [ RasMol ]  
    Ala D:429 - Thr D:430   [ RasMol ]  
 
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        Q7D2F4_AGRFC | Q7D2F4: 4zei
UniProtKB/TrEMBL
        Q7D2F4_AGRFC | Q7D2F4: 4ra1 4ze9 4zeb 4zec 4zed

(-) Related Entries Specified in the PDB File

4ra1